DOKK / manpages / debian 11 / nanofilt / NanoFilt.1.en
NANOFILT(1) User Commands NANOFILT(1)

NanoFilt - filtering and trimming of long read sequencing data

usage: NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH]

[--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC] [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP] [-s SUMMARY] [--readtype {1D,2D,1D2}] [input]

Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin.

show the help and exit
Print version and exit.
Specify the path and filename for the log file.
input, uncompressed fastq file

Filter on a minimum read length
Filter on a maximum read length
Filter on a minimum average read quality score
Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if using summary file.
Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if using summary file.

Trim n nucleotides from start of read
Trim n nucleotides from end of read

Use albacore or guppy summary file for quality scores
Which read type to extract information about from summary. Options are 1D, 2D or 1D2

gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam - gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz

The full documentation for NanoFilt is maintained as a Texinfo manual. If the info and NanoFilt programs are properly installed at your site, the command

info NanoFilt

should give you access to the complete manual.

June 2020 NanoFilt 2.6.0